Adding Jitter to Animation During High Velocity
There's possibly a script-level way of achieving this, but I strongly suggest trying the NLA(Non-Linear Animation) editor first.  It allows you to set F-Curve modifiers on-top of entire actions (so all the channels if need be).  Fairly quickly too.  Learning to use the NLA isn't too hard, and the payoff can be big, especially for the long animation you have.  Check out some basics of the NLA here: https://www.blender.org/manual/editors/nla.html

To get the jitter on certain parts of the animation, try adding a 'noise' modifier to the strip.  You could also try adding another animation layer 'on top' of your current one, and keyframe the noise on that strip instead, and then ease into it's influence using the Blend in/out fields.